From 91ca36cd73d5e200b7cb0442d7f4d13b0f68fd47 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Fri, 5 May 2017 18:40:15 -0400 Subject: [PATCH 1/4] Update description of HAPLOTYPE_MAP (1) Provide link to GATK forum article#9526. --- src/main/java/picard/fingerprint/CheckFingerprint.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/picard/fingerprint/CheckFingerprint.java b/src/main/java/picard/fingerprint/CheckFingerprint.java index 8bc4fbbcb..b09e8c8d1 100644 --- a/src/main/java/picard/fingerprint/CheckFingerprint.java +++ b/src/main/java/picard/fingerprint/CheckFingerprint.java @@ -103,7 +103,8 @@ "(VCF or BAM read group header) will be used.") public String EXPECTED_SAMPLE_ALIAS; - @Option(shortName="H", doc = "A file of haplotype information produced by the CheckFingerprint program.") + @Option(shortName="H", doc = "File that maps SNPs to blocks in high LD. See " + + "https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP; @Option(shortName="LOD", doc = "When counting haplotypes checked and matching, count only haplotypes " + From f019644480f3ab0237728d8dccde5f2a93894308 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Fri, 5 May 2017 18:42:31 -0400 Subject: [PATCH 2/4] Update HAPLOTYPE_MAP description (2) Provide link to GATK forum article#9526. --- src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java index e4c419f68..94cb18aff 100644 --- a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java +++ b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java @@ -62,7 +62,8 @@ doc="Optional output file to write metrics to. Default is to write to stdout.") public File OUTPUT; - @Option(shortName="H", doc="The file of haplotype data to use to pick SNPs to fingerprint") + @Option(shortName="H", doc="File that maps SNPs to blocks in high LD. See " + + "https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP; @Option(shortName="LOD", From ce9fe4f11bb8414cdc15d6d78e6e241113a45249 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Mon, 15 May 2017 11:53:51 -0400 Subject: [PATCH 3/4] Incorporate YF's suggestions to CheckFingerprint --- src/main/java/picard/fingerprint/CheckFingerprint.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/fingerprint/CheckFingerprint.java b/src/main/java/picard/fingerprint/CheckFingerprint.java index b09e8c8d1..2ca5fed61 100644 --- a/src/main/java/picard/fingerprint/CheckFingerprint.java +++ b/src/main/java/picard/fingerprint/CheckFingerprint.java @@ -103,7 +103,7 @@ "(VCF or BAM read group header) will be used.") public String EXPECTED_SAMPLE_ALIAS; - @Option(shortName="H", doc = "File that maps SNPs to blocks in high LD. See " + + @Option(shortName="H", doc = "The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " + "https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP; From 5e5af940b5d37f67dd5d611ec4dd64d4da5b0328 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Mon, 15 May 2017 11:55:14 -0400 Subject: [PATCH 4/4] Incorporate YF's suggestions to CrosscheckReadGroupFingerprints --- src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java index 94cb18aff..62696fdfe 100644 --- a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java +++ b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java @@ -62,7 +62,7 @@ doc="Optional output file to write metrics to. Default is to write to stdout.") public File OUTPUT; - @Option(shortName="H", doc="File that maps SNPs to blocks in high LD. See " + + @Option(shortName="H", doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " + "https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP;